Opened 22 months ago

Closed 22 months ago

#14383 closed defect (can't reproduce)

Crash in garbage collection while restoring session

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard, Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000000324fba000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000323fb7000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000322fb4000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000321fb1000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000320fae000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031ffab000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031efa8000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031dfa5000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031cfa2000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031bf9f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031af9c000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000319f99000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000318f96000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000317f93000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000316f90000 (most recent call first):
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000204859240 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334 in _qt_safe
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree (total: 61)


{"app_name":"ChimeraX","timestamp":"2024-01-15 22:10:58.00 +0000","app_version":"1.7.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.2.1 (23C71)","roots_installed":0,"name":"ChimeraX","incident_id":"A9BB8999-FB07-4A6C-8459-4E85AC447408"}
{
  "uptime" : 700000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,5",
  "coalitionID" : 109067,
  "osVersion" : {
    "train" : "macOS 14.2.1",
    "build" : "23C71",
    "releaseType" : "User"
  },
  "captureTime" : "2024-01-15 22:10:57.7385 +0000",
  "codeSigningMonitor" : 1,
  "incident" : "A9BB8999-FB07-4A6C-8459-4E85AC447408",
  "pid" : 81614,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-01-15 22:08:43.9115 +0000",
  "procStartAbsTime" : 16952727606138,
  "procExitAbsTime" : 16955938913629,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"13C36163-CC03-5074-9FDF-F7545CEC4403","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "F9070259-436C-FF97-23D6-B37F3ACB6C68",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 1065,
  "sleepWakeUUID" : "95A5E5B2-79E0-4A11-B417-45D68E7E9BE4",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140723233128279\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffcae528000-7ffcd6f40000 [650.1M] r-x\/r-x SM=COW  ...t_id=bdf72025",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":81614},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140723233128279\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      mapped file              7ffcae528000-7ffcd6f40000 [650.1M] r-x\/r-x SM=COW  ...t_id=bdf72025",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%)\nWritable regions: Total=3.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               128K        1 \nActivity Tracing                   256K        1 \nCG image                           224K       20 \nColorSync                          240K       30 \nCoreAnimation                      520K       55 \nCoreGraphics                        20K        3 \nCoreUI image data                 4500K       33 \nFoundation                          16K        1 \nKernel Alloc Once                    8K        1 \nMALLOC                             2.1G      130 \nMALLOC guard page                  384K       24 \nMach message                        16K        4 \nOpenGL GLSL                        256K        2 \nRosetta Arena                     4096K        2 \nRosetta Generic                   1596K      396 \nRosetta JIT                      128.0M        1 \nRosetta Return Stack              1100K      110 \nRosetta Thread Context            1100K      110 \nSTACK GUARD                         40K       10 \nStack                            403.2M       56 \nStack Guard                       56.2M       46 \nVM_ALLOCATE                      216.6M      330 \nVM_ALLOCATE (reserved)           256.1M       16         reserved VM address space (unallocated)\n__CTF                               824        1 \n__DATA                            55.9M      822 \n__DATA_CONST                      44.7M      427 \n__DATA_DIRTY                      1711K      226 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__LINKEDIT                       177.4M      184 \n__OBJC_RO                         71.1M        1 \n__OBJC_RW                         2166K        2 \n__TEXT                             1.0G      826 \ndyld private memory                516K        4 \nmapped file                        7.4G     1533 \nshared memory                     3532K       27 \nunshared pmap                     15.7M       10 \n===========                     =======  ======= \nTOTAL                             12.0G     5447 \nTOTAL, minus reserved VM space    11.8G     5447 \n",
  "legacyInfo" : {
  "threadTriggered" : {
    "name" : "CrBrowserMain",
    "queue" : "com.apple.main-thread"
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},
  "logWritingSignature" : "f06a03e30220641bd2e560ef258fb6240354f3f7",
  "trialInfo" : {
  "rollouts" : [
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      "factorPackIds" : {

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    },
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},
  "reportNotes" : [
  "PC register does not match crashing frame (0x0 vs 0x7FF8A913EA78)"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onepf.cxs"

Opened 188_b250.mrc as #2, grid size 250,250,250, pixel 0.826, shown at level
0.00373, step 1, values float32  
Log from Sun Jan 14 15:43:04 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-individuals.cxs" format session

Opened 188_b250.mrc as #2, grid size 250,250,250, pixel 0.826, shown at level
0.00373, step 1, values float32  
Log from Sun Jan 14 14:55:25 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit-240114.cxs" format session

Opened postprocess_masked330_onepf.mrc as #6, grid size 274,274,274, pixel
1.51, shown at level 0.0124, step 2, values float32  
Log from Sun Jan 14 14:18:05 2024UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-27.cxs" format session

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0195, step 1, values float32  
Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at
level 0.0174, step 1, values float32  
Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0209, step 1, values float32  
Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at level 0.0176, step 1, values float32  
Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51,
shown at level 0.0104, step 2, values float32  
Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel
1.51, shown at level 0.00964, step 1, values float32  
Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel
1.51, shown at level 0.0121, step 1, values float32  
Opened postprocess_masked330.mrc y flip copy as #2.1.1.1, grid size
274,274,274, pixel 1.51, shown at level 0.0202, step 1, values float32  
Log from Fri Jan 12 07:27:46 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit14-20.cxs" format session

Opened post266.mrc as #1, grid size 274,274,274, pixel 1.51, shown at level
0.0195, step 1, values float32  
Opened post266flipy.mrc as #3, grid size 274,274,274, pixel 1.51, shown at
level 0.0174, step 1, values float32  
Opened post266flipy.mrc as #4, grid size 274,274,274, pixel 1.51, shown at
level 0.0209, step 1, values float32  
Opened post266flipy.mrc copy as #6, grid size 274,274,274, pixel 1.51, shown
at level 0.0176, step 1, values float32  
Opened postprocess_masked330.mrc as #5, grid size 274,274,274, pixel 1.51,
shown at level 0.0104, step 2, values float32  
Opened postprocess_masked330.mrc y flip as #7, grid size 274,274,274, pixel
1.51, shown at level 0.00964, step 1, values float32  
Opened postprocess_masked330_onepf.mrc as #8, grid size 274,274,274, pixel
1.51, shown at level 0.014, step 1, values float32  
Opened postprocess_masked330.mrc y flip copy as #2.1.1.1, grid size
274,274,274, pixel 1.51, shown at level 0.0202, step 1, values float32  
Log from Wed Jan 10 14:43:33 2024UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

[deleted to fit within ticket limits]

> show cartoons

> show atoms

> delete atoms sel

> delete bonds sel

> delete atoms sel

> delete bonds sel

> hide atoms

> hide cartoons

> show cartoons

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> ui tool show Matchmaker

> hide #!2 models

> matchmaker #2/G to #1/G pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-
rechained.pdb, chain G (#1) with pointy-1pf-relative-rechained.pdb, chain G
(#2), sequence alignment score = 573.4  
RMSD between 71 pruned atom pairs is 0.804 angstroms; (across all 111 pairs:
3.894)  
  

> show #!2 models

> morph

Missing or invalid "structures" argument: empty atom specifier  

> morph #1.2

Require at least 2 structures for morph  

> morph #1 #2

Computed 51 frame morph #3  

> coordset #3 1,51

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> morph #2 #1

Computed 51 frame morph #4  

> coordset #4 1,51

> hide #!3 models

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> select #2/A

265 atoms, 264 bonds, 19 residues, 1 model selected  

> color #2/A corflower blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #2/A bychain corflower blue

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color

> color /A blue

> color /A cornflower blue

[Repeated 1 time(s)]

> color /B medium turquoise

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E peach puff

> color /F plum

> color /G medium orchid

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E peach puff

> color /F plum

> color /G slate blue

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E peach puff

> color /F plum

> color /G slate blue

> color /H lavender

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E peach puff

> color /F plum

> color /G slate blue

> color /H lavender

> color /I salmon

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E goldenrod

> color /F plum

> color /G slate blue

> color /H lavender

> color /I salmon

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E goldenrod

> color /F plum

> color /G dark cyan

> color /H lavender

> color /I salmon

> color /A cornflower blue

> color /B medium turquoise

> color /C medium sea green

> color /D pale goldenrod

> color /E goldenrod

> color /F plum

> color /G hot pink

> color /H lavender

> color /I salmon

> morph

Missing or invalid "structures" argument: empty atom specifier  

> morph #2 #1 wrap true

Computed 101 frame morph #5  

> coordset #5 1,101

> hide #!4 models

> lighting soft

> set bgColor white

> cartoon style coil width 1.5 thickness 0.8

> cartoon style helix xsection round width 3 thickness 0.8

> cartoon style strand xsection round width 3 thickness 0.8

> cartoon style strand arrowScale 1

> cartoon style helix xsection oval sides 10

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.003

> lighting msDepthBias 0.004

> lighting shadows true intensity 0.06

> lighting depthCueColor #000000

> movie record

> movie encode /Users/chaaban/Desktop/movie.mp4 framerate 25.0

Movie saved to /Users/chaaban/Desktop/movie.mp4  
  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/postprocess_masked330_onepf.mrc"

Opened postprocess_masked330_onepf.mrc as #6, grid size 274,274,274, pixel
1.51, shown at level 9.42e-06, step 2, values float32  

> volume #6 level 0.01241

> hide #!6 models

> hide #!5 models

> show #!6 models

> show #!1 models

> hide #!1 models

> show #!1 models

> ui tool show "Fit in Map"

> fitmap #1 inMap #6

Fit molecule Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb
(#1) to map postprocess_masked330_onepf.mrc (#6) using 6218 atoms  
average map value = 0.01328, steps = 40  
shifted from previous position = 0.162  
rotated from previous position = 0.147 degrees  
atoms outside contour = 3565, contour level = 0.012408  
  
Position of Fit14-27-1-stitchedtemp3-lightrefine4-newrefinedpf-
alsoneighbour-2-refined-2-fixcrosshelix-3-refined-4-replacefirst-rechained.pdb
(#1) relative to postprocess_masked330_onepf.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99999701 -0.00172986 0.00172963 0.05739393  
0.00173119 0.99999820 -0.00077010 -0.06466265  
-0.00172830 0.00077310 0.99999821 0.15764343  
Axis 0.30081486 0.67405099 0.67465968  
Axis point 68.53340975 19.14218260 0.00000000  
Rotation angle (degrees) 0.14696576  
Shift along axis 0.08003468  
  

> transparency #1,6 50

> ui tool show "Hide Dust"

> surface dust #6 size 9.04

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit-240114.cxs"

——— End of log from Sun Jan 14 14:18:05 2024 ———

opened ChimeraX session  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Fit-240114-back.png" width 1600 transparentBackground
> true

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/188.cif"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/188.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 188.cif #7  
---  
Chain | Description  
A0 | No description available  
A1 | No description available  
A2 | No description available  
A3 | No description available  
A4 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
Aa | No description available  
Aaa | No description available  
Aab | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ak | No description available  
Al | No description available  
Am | No description available  
An | No description available  
Ao | No description available  
Ap | No description available  
Aq | No description available  
Ar | No description available  
As | No description available  
At | No description available  
Au | No description available  
Av | No description available  
Aw | No description available  
Ax | No description available  
Ay | No description available  
Az | No description available  
  

> hide #!6 models

> hide #!1 models

> show #!1 models

> close session

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/188.cif" format mmcif

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/188.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 188.cif #1  
---  
Chain | Description  
A0 | No description available  
A1 | No description available  
A2 | No description available  
A3 | No description available  
A4 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
Aa | No description available  
Aaa | No description available  
Aab | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ak | No description available  
Al | No description available  
Am | No description available  
An | No description available  
Ao | No description available  
Ap | No description available  
Aq | No description available  
Ar | No description available  
As | No description available  
At | No description available  
Au | No description available  
Av | No description available  
Aw | No description available  
Ax | No description available  
Ay | No description available  
Az | No description available  
  

> hide atoms

> show cartoons

> preset custom clean-chain

Using preset: Custom / Clean-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain
    ui windowfill true

  

> ui windowfill toggle

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/188_b250.mrc"

Opened 188_b250.mrc as #2, grid size 250,250,250, pixel 0.826, shown at level
0.00707, step 1, values float32  

> hide cartoons

> show atoms

> style stick

Changed 20272 atom styles  

> transparency 50

> ui mousemode right zoom

> ui mousemode right "rotate selected models"

> ui mousemode right zoom

> ui tool show "Color Zone"

> color zone #2 near #1 distance 4.96

> transparency 50

> select clear

> lighting depthCueColor #999999

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114.csx"

No known data format for file suffix '.csx'  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114.cxs"

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-fitmap.png" width 1600
> transparentBackground true

> hide #!1 models

> transparency #2 0

> view

> ui tool show "Hide Dust"

> surface dust #2 size 4.96

> volume #2 level 0.006833

> volume #2 level 0.006236

> surface dust #2 size 4.96

> transparency #2 50

> select clear

> transparency #2 0

> color zone #2 near #1 distance 4.96

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-map.png" width 1600
> transparentBackground true

> show #!1 models

> transparency 50

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-map-withfit.png" width 1600
> transparentBackground true

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114.cxs"

> color byhetero

> hide #!1 models

> show #!1 models

> hide #!2 models

> show cartoons

> view sel

> show #!2 models

> select clear

> volume #2 level 0.004206

> transparency 50

> view

> color zone #2 near #1 distance 4.96

> select clear

> preset custom pretty-chain

Using preset: Custom / Pretty-chain  
Preset expands to these ChimeraX commands:

    
    
    lighting soft
    set bgColor white
    cartoon style coil width 1.5 thickness 0.8
    cartoon style helix xsection round width 3 thickness 0.8
    cartoon style strand xsection round width 3 thickness 0.8
    cartoon style strand arrowscale 1
    cartoon style helix xsection oval sides 10
    graphics silhouettes true
    graphics silhouettes width 1.5
    graphics silhouettes depthJump 0.003
    lighting msDepthBias 0.004
    lighting shadows true intensity 0.06
    lighting depthCueColor #000000
    color bychain

  

> color zone #2 near #1 distance 4.96

> volume splitbyzone #2

Opened 188_b250.mrc 0 as #3.1, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 1 as #3.2, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 2 as #3.3, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 3 as #3.4, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 4 as #3.5, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 5 as #3.6, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 6 as #3.7, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 7 as #3.8, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 8 as #3.9, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 9 as #3.10, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 10 as #3.11, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 11 as #3.12, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 12 as #3.13, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 13 as #3.14, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 14 as #3.15, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 15 as #3.16, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 16 as #3.17, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 17 as #3.18, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 18 as #3.19, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 19 as #3.20, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 20 as #3.21, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 21 as #3.22, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 22 as #3.23, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 23 as #3.24, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 24 as #3.25, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 25 as #3.26, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 26 as #3.27, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 27 as #3.28, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 28 as #3.29, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 29 as #3.30, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 30 as #3.31, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 31 as #3.32, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 32 as #3.33, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 33 as #3.34, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 34 as #3.35, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 35 as #3.36, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 36 as #3.37, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 37 as #3.38, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  
Opened 188_b250.mrc 38 as #3.39, grid size 250,250,250, pixel 0.826, shown at
level 0.00421, step 1, values float32  

> hide #!3.1-36 target m

> hide #!1 models

> hide #!3.37 models

> hide #!3.38 models

> hide #!3.39 models

> show #!3.37 models

> hide #!3.37 models

> show #!3.36 models

> hide #!3.36 models

> show #!3.35 models

> hide #!3.35 models

> show #!3.34 models

> hide #!3.34 models

> show #!3.33 models

> hide #!3.33 models

> show #!3.32 models

> hide #!3.32 models

> show #!3.31 models

> hide #!3.31 models

> show #!3.30 models

> hide #!3.30 models

> show #!3.29 models

> hide #!3.29 models

> show #!3.28 models

> hide #!3.28 models

> show #!3.27 models

> hide #!3.27 models

> show #!3.26 models

> hide #!3.26 models

> show #!3.25 models

> hide #!3.25 models

> show #!3.24 models

> hide #!3.24 models

> show #!3.23 models

> hide #!3.23 models

> show #!3.22 models

> hide #!3.22 models

> show #!3.21 models

> hide #!3.21 models

> show #!3.20 models

> hide #!3.20 models

> show #!3.19 models

> hide #!3.19 models

> show #!3.18 models

> hide #!3.18 models

> show #!3.17 models

> hide #!3.17 models

> show #!3.16 models

> hide #!3.16 models

> show #!3.15 models

> hide #!3.15 models

> show #!3.14 models

> hide #!3.14 models

> show #!3.13 models

> hide #!3.13 models

> show #!3.12 models

> hide #!3.12 models

> show #!3.11 models

> hide #!3.11 models

> show #!3.10 models

> hide #!3.10 models

> show #!3.9 models

> hide #!3.9 models

> show #!3.8 models

> hide #!3.8 models

> show #!3.7 models

> hide #!3.7 models

> show #!3.7 models

> hide #!3.7 models

> show #!3.6 models

> hide #!3.6 models

> show #!3.5 models

> hide #!3.5 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.2 models

> hide #!3.2 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.5 models

> hide #!3.5 models

> show #!1 models

> close #3

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.003848

> volume #2 level 0.003729

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select add #1

20272 atoms, 20308 bonds, 2600 residues, 1 model selected  

> color sel bypolymer

> select subtract #1

Nothing selected  

> color bychain

> hide atoms

> show cartoons

> color sel light sea green

> ui tool show "Color Actions"

> color sel lavender

> color sel pale goldenrod

> color sel alice blue

> color sel azure

> color sel light steel blue

> color sel aquamarine

> color sel sky blue

> select ~sel

10240 atoms, 10261 bonds, 1314 residues, 3 models selected  

> color sel violet

> select clear

> undo

> select clear

[Repeated 2 time(s)]

> color sel pale turquoise

> color sel light sky blue

> select ~sel

9985 atoms, 10001 bonds, 1278 residues, 3 models selected  

> color sel violet

> color sel plum

> color sel violet

> color sel cornsilk

> color sel lemon chiffon

> color sel navajo white

> color sel peach puff

[Repeated 1 time(s)]

> color sel pink

> color sel misty rose

> color sel bisque

> color sel light pink

> color sel light coral

> color sel magenta

> color sel pale violet red

> color sel light coral

> color sel wheat

> color sel honeydew

> color sel pale goldenrod

> color sel violet

> color sel pale goldenrod

> select clear

> color sel light blue

> color sel light sky blue

> select clear

> show cartoons

> redo

> undo

> combine sel

> select ~sel

30573 atoms, 30625 bonds, 3924 residues, 2 models selected  

> select subtract #3

10301 atoms, 10317 bonds, 1324 residues, 1 model selected  

> combine sel

> hide #!1 models

> select add #1

20272 atoms, 20308 bonds, 2600 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #4

20272 atoms, 20308 bonds, 2600 residues, 1 model selected  

> hide #!4 models

> show #!4 models

> hide sel cartoons

> hide #!4 models

> hide #!3 models

> color sel wheat

> color sel khaki

> color sel pale goldenrod

> color sel light goldenrod yellow

> color sel yellow

> color sel khaki

> color sel antique white

> color sel old lace

> color sel light pink

> color sel lemon chiffon

> color sel ivory

> color sel white

> select clear

> undo

> color sel light yellow

> select clear

> select ~sel

50845 atoms, 50933 bonds, 6524 residues, 5 models selected  

> select subtract #4

30573 atoms, 30625 bonds, 3924 residues, 4 models selected  

> select subtract #3

10301 atoms, 10317 bonds, 1324 residues, 3 models selected  

> select subtract #2

10301 atoms, 10317 bonds, 1324 residues, 1 model selected  

> show sel cartoons

> select ~sel

50515 atoms, 50605 bonds, 6476 residues, 5 models selected  

> hide sel & #!1 cartoons

> select clear

> color sel cornflower blue

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-individuals.cxs"

——— End of log from Sun Jan 14 14:55:25 2024 ———

opened ChimeraX session  

> close #3-4

> select clear

> show cartoons

> combine #1

> select #3/Ad

985 atoms, 990 bonds, 126 residues, 1 model selected  

> select ~sel

39559 atoms, 39626 bonds, 5074 residues, 4 models selected  

> select subtract #1

19287 atoms, 19318 bonds, 2474 residues, 3 models selected  

> select subtract #2

19287 atoms, 19318 bonds, 2474 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #1/Aj

482 atoms, 483 bonds, 63 residues, 1 model selected  

> select ~sel

20775 atoms, 20815 bonds, 2663 residues, 4 models selected  

> select subtract #3

19790 atoms, 19825 bonds, 2537 residues, 3 models selected  

> select subtract #2

19790 atoms, 19825 bonds, 2537 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show Matchmaker

> matchmaker #1/Aj to #3/Ad pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker copy of 188.cif, chain Ad (#3) with 188.cif, chain Aj (#1),
sequence alignment score = 122  
RMSD between 25 pruned atom pairs is 0.122 angstroms; (across all 25 pairs:
0.122)  
  

> select clear

> delete atoms sel

> delete bonds sel

> delete atoms sel

> delete bonds sel

> delete atoms sel

> delete bonds sel

> color sel cornflower blue

> select clear

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onesubunit.cxs"

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/188.cif"

Summary of feedback from opening /Users/chaaban/Library/CloudStorage/OneDrive-
MRCLaboratoryofMolecularBiology/Documents/Carter Lab/Diorge/Membranes/188.cif  
---  
warnings | Missing entity information. Treating each chain as a separate
entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for 188.cif #4  
---  
Chain | Description  
A0 | No description available  
A1 | No description available  
A2 | No description available  
A3 | No description available  
A4 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
Aa | No description available  
Aaa | No description available  
Aab | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ak | No description available  
Al | No description available  
Am | No description available  
An | No description available  
Ao | No description available  
Ap | No description available  
Aq | No description available  
Ar | No description available  
As | No description available  
At | No description available  
Au | No description available  
Av | No description available  
Aw | No description available  
Ax | No description available  
Ay | No description available  
Az | No description available  
  

> hide atoms

> show cartoons

> combine #1,3

[Repeated 5 time(s)]

> hide #!5-10 target m

> hide #!1 models

> hide #!4 models

> hide #!3 models

> show #!4 models

> show #!5 models

> hide #!4 models

> mmaker #5/Ad to #4/A[

No 'to' model specified  

> mmaker #5/Ad to #4/Ap

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ap (#4) with combination, chain Ad (#5), sequence
alignment score = 65.8  
RMSD between 15 pruned atom pairs is 0.182 angstroms; (across all 15 pairs:
0.182)  
  

> show #!4 models

> mmaker #6/Ad to #4/Af

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Af (#4) with combination, chain Ad (#6), sequence
alignment score = 168.3  
RMSD between 35 pruned atom pairs is 0.095 angstroms; (across all 35 pairs:
0.095)  
  

> show #!6 models

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> select ~sel & ##selected

Nothing selected  

> mmaker #7/Ad to #4/Ae

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ae (#4) with combination, chain Ad (#7), sequence
alignment score = 601.3  
RMSD between 115 pruned atom pairs is 0.134 angstroms; (across all 121 pairs:
1.198)  
  

> show #!7 models

> mmaker #7/Ad to #4/At

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain At (#4) with combination, chain Ad (#7), sequence
alignment score = 283.5  
RMSD between 57 pruned atom pairs is 0.084 angstroms; (across all 57 pairs:
0.084)  
  

> mmaker #8/Ad to #4/Ae

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ae (#4) with combination, chain Ad (#8), sequence
alignment score = 601.3  
RMSD between 115 pruned atom pairs is 0.134 angstroms; (across all 121 pairs:
1.198)  
  

> show #!8 models

> mmaker #9/Ad to #4/Ad

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ad (#4) with combination, chain Ad (#9), sequence
alignment score = 646.7  
RMSD between 126 pruned atom pairs is 0.000 angstroms; (across all 126 pairs:
0.000)  
  

> show #!9 models

> mmaker #10/Ad to #4/Ab

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ab (#4) with combination, chain Ad (#10), sequence
alignment score = 505.8  
RMSD between 100 pruned atom pairs is 0.246 angstroms; (across all 103 pairs:
0.930)  
  

> show #!10 models

> hide #!4 models

> lighting soft

> set bgColor white

> cartoon style coil width 1.5 thickness 0.8

> cartoon style helix xsection round width 3 thickness 0.8

> cartoon style strand xsection round width 3 thickness 0.8

> cartoon style strand arrowScale 1

> cartoon style helix xsection oval sides 10

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.003

> lighting msDepthBias 0.004

> lighting shadows true intensity 0.06

> lighting depthCueColor #000000

> color sel bychain

> color #5 #8efa00ff

> color #5 #0096ffff

> color #6 #d783ffff

> color #7 #ff2f92ff

> color #8 #942193ff

> color #9 #00fa92ff

> color #9 #009193ff

> color #9 #8efa00ff

> color #9 #008f00ff

> color #9 #4f8f00ff

> color #9 #009051ff

> color #9 #009193ff

> color #10 #00f900ff

> color #10 #008f00ff

> color #10 #929000ff

> color #10 #4f8f00ff

> color #10 #008f00ff

> color #10 #009051ff

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onepf.cxs"

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onepf.png" width 1600
> transparentBackground true

> show #!4 models

> hide #!4 models

> combine #1,3

> show #!4 models

> mmaker #11/Ad to #4/Ao

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ao (#4) with combination, chain Ad (#11), sequence
alignment score = 287.7  
RMSD between 60 pruned atom pairs is 0.275 angstroms; (across all 63 pairs:
1.143)  
  

> hide #!4 models

> color #11 #73fcd6ff

> color #11 #73fa79ff

> mmaker #11/Ad to #4/Ao

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 188.cif, chain Ao (#4) with combination, chain Ad (#11), sequence
alignment score = 287.7  
RMSD between 60 pruned atom pairs is 0.275 angstroms; (across all 63 pairs:
1.143)  
  

> lighting soft

> set bgColor white

> cartoon style coil width 1.5 thickness 0.8

> cartoon style helix xsection round width 3 thickness 0.8

> cartoon style strand xsection round width 3 thickness 0.8

> cartoon style strand arrowScale 1

> cartoon style helix xsection oval sides 10

> graphics silhouettes true

> graphics silhouettes width 1.5

> graphics silhouettes depthJump 0.003

> lighting msDepthBias 0.004

> lighting shadows true intensity 0.06

> lighting depthCueColor #000000

> select clear

> save "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-onepf.cxs"

——— End of log from Sun Jan 14 15:43:04 2024 ———

opened ChimeraX session  

> ui tool show "Show Sequence Viewer"

> sequence chain #1/Aj #4/Aj #5/Aj #6/Aj #7/Aj #8/Aj #9/Aj #10/Aj #11/Aj

Alignment identifier is 1  

> select #7/Aj:147

8 atoms, 7 bonds, 1 residue, 1 model selected  

> open "/Users/chaaban/Library/CloudStorage/OneDrive-
> MRCLaboratoryofMolecularBiology/Documents/Carter
> Lab/Diorge/Membranes/Filament-240114-individuals.cxs"


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac14,5
      Model Number: Z17J0018AB/A
      Chip: Unknown
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.61.4
      OS Loader Version: 10151.61.4

Software:

    System Software Overview:

      System Version: macOS 14.2.1 (23C71)
      Kernel Version: Darwin 23.2.0
      Time since boot: 10 days, 14 hours, 40 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.3
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 22 months ago

Cc: Tom Goddard Greg Couch added
Component: Unassigned → Core
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection while restoring session

comment:2 by Eric Pettersen, 22 months ago

Resolution: → can't reproduce
Status: accepted → closed
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